I’m not an expert on this but it does sound as if you have a few things to sort out. Carte de séjour applications are not just a formality, they are studied quite carefully; there are boxes you need to tick and if you don’t tick them there is a real danger of being refused.
I guess the reason you’re being asked for your attestations is that you need to prove residence in France, and in order to be officially classed as resident you need to show you have had healthcare in place continuously since you arrived, because this is one of France’s conditions for “legal and stable residence”. The “attestation” they are asking for is the certificate your healthcare caisse issues when your entitlement starts, stating the date on which your rights were opened, and also the date on which they end if for some reason your cover has a time limit on it. Do neither of you in fact currently have any health cover at all in place in France? If you’ve been living here since December but without health cover, the préfecture may decide that you have been here irregularly during this period since the conditions for residence weren’t being met.
I’m not quite sure what the point would be of going the UK to get your OH’s UK national insurance number? Membership of the UK social security system and the NHS is reserved for UK residents only, and your OH’s entitlement to NHS cover automatically ceased when he left the UK to live in France. If he doesn’t have any current EU health cover he’s not actually entitled to go back to the UK and see a doctor. If in fact he’s a posted worker or a UK pensioner with an S1 he should have taken his S1 to CPAM, but from what you say it doesn’t sound as if he is.
The préfecture is asking both of you to prove your entitlement to healthcare, and micro entrepreneur is designed as, and works best as, a one-person business, ie one person runs it and one person obtains health cover. There are options to run a micro as a married couple in which case the spouse has a choice of registering as either a conjoint collaborateur or a conjoint salarié, and most people choose conjoint collaborateur. I don’t see how you could be registered as a salarié as a non-EU citizen without a carte de séjour that permits you to work in France, but whether you need a carte de séjour in order to be registered as a conjoint collaborateur, I don’t know. But in any case, to my mind once you start running a micro as a couple the scheme starts losing its advantages. Depending on your circumstances, micro might still be the best option but you should consider the alternatives and choose the statut that will be best in the long term, rather than rush into registering a micro now and find out further down the line that it was an expensive mistake and you’re paying higher cotisations than you would have under another setup.
You say you’ve already started earning an income from the gite, and it sounds as if this is your main source of income. Is it not registered as a business at all, as yet? Obviously we don’t know the full circumstances but on the face of it, it sounds irregular to be earning your main income from an unregistered business activity. If that is the case you should decide quickly on how to register it and get it sorted, because if the préfecture picks up on irregularities on your carte de séjour application you risk all kinds of queries coming at you.
Don’t take this as “advice” because I don’t know the answers, but I would have thought these are the issues you should be addressing, hope this helps.